Aligment rate vs called peaks

Question

[sahhomaha]

Hi. I need help to understand why I got this technical issue in my chip seq data. The first chip replicate the alignment read was 66% and when I used mas2 to call peaks I got 46000 peaks. Which considered poor. The secound time i got only 800 peaks BUT the alignment read was : any one can ecplain why there is no peacks ? Thank you MCF7IGF109859

69925474 reads; of these:
  69925474 (100.00%) were unpaired; of these:
    15892074 (22.73%) aligned 0 times
    41130769 (58.82%) aligned exactly 1 time
    12902631 (18.45%) aligned >1 times
77.27% overall alignment rate

69078260 reads; of these:
  69078260 (100.00%) were unpaired; of these:
    15240704 (22.06%) aligned 0 times
    40669901 (58.88%) aligned exactly 1 time
    13167655 (19.06%) aligned >1 times
77.94% overall alignment rate

[colindaven]

In short - no. More detail needed. genome, read length, goal, antibody, etc etc etc etc.

Have a look at Deeptools in Freiburg and especially their excellent plotFingerprint plots to assess your ChIP signal.